A 1-year-old male Cairn Terrier was evaluated for chronic coughing that was aggravated by eating or drinking. Radiography revealed an esophageal diverticulum, regional megaesophagus, and focal interstitial densities in the right caudal and middle lung lobes. Using fluoroscopy and contrast radiography, contrast material was seen to accumulate in the diverticulum and to reflux into the right middle, caudal, and accessory bronchi. Radiographic diagnosis was bronchoesophageal fistula. Via right eighth intercostal space thoracotomy, the abnormal connection between esophagus and caudal lobe of the right lung was identified, the lobe was resected, and the esophagus was closed. Histologic examination of the connecting tissue revealed a lining of stratified epithelium, with the superficial layer being predominantly ciliated columnar epithelium. Several findings led to the conclusion that the fistula was a congenital lesion, arising from aberrant formation of the respiratory tract from the embryologic digestive tract. Histologic examination revealed smooth muscle and lack of inflammation in tissue surrounding the fistula, which are criteria for identifying congenital bronchoesophageal fistula in human patients. The dog was young and did not have a history of esophageal foreign bodies. Postoperative complications were not encountered, and 9 months later, the dog was reported to be eating dry dog food without coughing. Congenital and acquired bronchoesophageal fistulas in dogs are reported infrequently. Furthermore, 2 of 12 previously reported bronchoesophageal fistulas in dogs, one of which was considered congenital, developed in Cairn Terriers.